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Montgomery J, Morran S, MacGregor DR, McElroy JS, Neve P, Neto C, Vila-Aiub MM, Sandoval MV, Menéndez AI, Kreiner JM, Fan L, Caicedo AL, Maughan PJ, Martins BAB, Mika J, Collavo A, Merotto A, Subramanian NK, Bagavathiannan MV, Cutti L, Islam MM, Gill BS, Cicchillo R, Gast R, Soni N, Wright TR, Zastrow-Hayes G, May G, Malone JM, Sehgal D, Kaundun SS, Dale RP, Vorster BJ, Peters B, Lerchl J, Tranel PJ, Beffa R, Fournier-Level A, Jugulam M, Fengler K, Llaca V, Patterson EL, Gaines TA. Current status of community resources and priorities for weed genomics research. Genome Biol 2024; 25:139. [PMID: 38802856 PMCID: PMC11129445 DOI: 10.1186/s13059-024-03274-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 05/13/2024] [Indexed: 05/29/2024] Open
Abstract
Weeds are attractive models for basic and applied research due to their impacts on agricultural systems and capacity to swiftly adapt in response to anthropogenic selection pressures. Currently, a lack of genomic information precludes research to elucidate the genetic basis of rapid adaptation for important traits like herbicide resistance and stress tolerance and the effect of evolutionary mechanisms on wild populations. The International Weed Genomics Consortium is a collaborative group of scientists focused on developing genomic resources to impact research into sustainable, effective weed control methods and to provide insights about stress tolerance and adaptation to assist crop breeding.
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Affiliation(s)
- Jacob Montgomery
- Department of Agricultural Biology, Colorado State University, 1177 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Sarah Morran
- Department of Agricultural Biology, Colorado State University, 1177 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Dana R MacGregor
- Protecting Crops and the Environment, Rothamsted Research, Harpenden, Hertfordshire, UK
| | - J Scott McElroy
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, USA
| | - Paul Neve
- Department of Plant and Environmental Sciences, University of Copenhagen, Taastrup, Denmark
| | - Célia Neto
- Department of Plant and Environmental Sciences, University of Copenhagen, Taastrup, Denmark
| | - Martin M Vila-Aiub
- IFEVA-Conicet-Department of Ecology, University of Buenos Aires, Buenos Aires, Argentina
| | | | - Analia I Menéndez
- Department of Ecology, Faculty of Agronomy, University of Buenos Aires, Buenos Aires, Argentina
| | - Julia M Kreiner
- Department of Botany, The University of British Columbia, Vancouver, BC, Canada
| | - Longjiang Fan
- Institute of Crop Sciences, Zhejiang University, Hangzhou, China
| | - Ana L Caicedo
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Peter J Maughan
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | | | - Jagoda Mika
- Bayer AG, Weed Control Research, Frankfurt, Germany
| | | | - Aldo Merotto
- Department of Crop Sciences, Federal University of Rio Grande Do Sul, Porto Alegre, Rio Grande Do Sul, Brazil
| | - Nithya K Subramanian
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA
| | | | - Luan Cutti
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | | | - Bikram S Gill
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Robert Cicchillo
- Crop Protection Discovery and Development, Corteva Agriscience, Indianapolis, IN, USA
| | - Roger Gast
- Crop Protection Discovery and Development, Corteva Agriscience, Indianapolis, IN, USA
| | - Neeta Soni
- Crop Protection Discovery and Development, Corteva Agriscience, Indianapolis, IN, USA
| | - Terry R Wright
- Genome Center of Excellence, Corteva Agriscience, Johnston, IA, USA
| | | | - Gregory May
- Genome Center of Excellence, Corteva Agriscience, Johnston, IA, USA
| | - Jenna M Malone
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, South Australia, Australia
| | - Deepmala Sehgal
- Jealott's Hill International Research Centre, Syngenta Ltd, Bracknell, Berkshire, UK
| | - Shiv Shankhar Kaundun
- Jealott's Hill International Research Centre, Syngenta Ltd, Bracknell, Berkshire, UK
| | - Richard P Dale
- Jealott's Hill International Research Centre, Syngenta Ltd, Bracknell, Berkshire, UK
| | - Barend Juan Vorster
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Bodo Peters
- Bayer AG, Weed Control Research, Frankfurt, Germany
| | | | - Patrick J Tranel
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Roland Beffa
- Senior Scientist Consultant, Herbicide Resistance Action Committee / CropLife International, Liederbach, Germany
| | | | - Mithila Jugulam
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - Kevin Fengler
- Genome Center of Excellence, Corteva Agriscience, Johnston, IA, USA
| | - Victor Llaca
- Genome Center of Excellence, Corteva Agriscience, Johnston, IA, USA
| | - Eric L Patterson
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Todd A Gaines
- Department of Agricultural Biology, Colorado State University, 1177 Campus Delivery, Fort Collins, CO, 80523, USA.
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2
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Paterson AH, Queitsch C. Genome organization and botanical diversity. THE PLANT CELL 2024; 36:1186-1204. [PMID: 38382084 PMCID: PMC11062460 DOI: 10.1093/plcell/koae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 02/07/2024] [Accepted: 02/07/2024] [Indexed: 02/23/2024]
Abstract
The rich diversity of angiosperms, both the planet's dominant flora and the cornerstone of agriculture, is integrally intertwined with a distinctive evolutionary history. Here, we explore the interplay between angiosperm genome organization and botanical diversity, empowered by genomic approaches ranging from genetic linkage mapping to analysis of gene regulation. Commonality in the genetic hardware of plants has enabled robust comparative genomics that has provided a broad picture of angiosperm evolution and implicated both general processes and specific elements in contributing to botanical diversity. We argue that the hardware of plant genomes-both in content and in dynamics-has been shaped by selection for rather substantial differences in gene regulation between plants and animals such as maize and human, organisms of comparable genome size and gene number. Their distinctive genome content and dynamics may reflect in part the indeterminate development of plants that puts strikingly different demands on gene regulation than in animals. Repeated polyploidization of plant genomes and multiplication of individual genes together with extensive rearrangement and differential retention provide rich raw material for selection of morphological and/or physiological variations conferring fitness in specific niches, whether natural or artificial. These findings exemplify the burgeoning information available to employ in increasing knowledge of plant biology and in modifying selected plants to better meet human needs.
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Affiliation(s)
- Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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3
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Evalen PS, Barnhardt EN, Ryu J, Stahlschmidt ZR. Toxicity of glyphosate to animals: A meta-analytical approach. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 347:123669. [PMID: 38460584 DOI: 10.1016/j.envpol.2024.123669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/10/2024] [Accepted: 02/26/2024] [Indexed: 03/11/2024]
Abstract
Glyphosate (GLY)-based herbicides (GBHs) are the most commonly applied pesticide worldwide, and non-target organisms (e.g., animals) are now regularly exposed to GLY and GBHs due to the accumulation of these chemicals in many environments. Although GLY/GBH was previously considered to be non-toxic, growing evidence indicates that GLY/GBH negatively affects some animal taxa. However, there has been no systematic analysis quantifying its toxicity to animals. Therefore, we used a meta-analytical approach to determine whether there is a demonstrable effect of GLY/GBH toxicity across animals. We further addressed whether the effects of GLY/GBH vary due to (1) taxon (invertebrate vs. vertebrate), (2) habitat (aquatic vs. terrestrial), (3) type of biological response (behavior vs. physiology vs. survival), and (4) dosage or concentration of GLY/GBH. Using this approach, we also determined whether adjuvants (e.g., surfactants) in commercial formulations of GBHs increased toxicity for animals relative to exposure to GLY alone. We analyzed 1282 observations from 121 articles. We conclude that GLY is generally sub-lethally toxic for animals, particularly for animals in aquatic or marine habitats, and that toxicity did not exhibit dose-dependency. Yet, our analyses detected evidence for widespread publication bias so we encourage continued experimental investigations to better understand factors influencing GLY/GBH toxicity to animals.
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Affiliation(s)
- P S Evalen
- University of the Pacific, Stockton, CA, USA; University of Pennsylvania, Philadelphia, PA, USA
| | | | - J Ryu
- University of the Pacific, Stockton, CA, USA
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4
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Claret JL, Di-Liegro M, Namias A, Assogba B, Makoundou P, Koffi A, Pennetier C, Weill M, Milesi P, Labbé P. Despite structural identity, ace-1 heterogenous duplication resistance alleles are quite diverse in Anopheles mosquitoes. Heredity (Edinb) 2024; 132:179-191. [PMID: 38280976 PMCID: PMC10997782 DOI: 10.1038/s41437-024-00670-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/08/2024] [Accepted: 01/11/2024] [Indexed: 01/29/2024] Open
Abstract
Anopheles gambiae s.l. has been the target of intense insecticide treatment since the mid-20th century to try and control malaria. A substitution in the ace-1 locus has been rapidly selected for, allowing resistance to organophosphate and carbamate insecticides. Since then, two types of duplication of the ace-1 locus have been found in An. gambiae s.l. populations: homogeneous duplications that are composed of several resistance copies, or heterogeneous duplications that contain both resistance and susceptible copies. The substitution induces a trade-off between resistance in the presence of insecticides and disadvantages in their absence: the heterogeneous duplications allow the fixation of the intermediate heterozygote phenotype. So far, a single heterogeneous duplication has been described in An. gambiae s.l. populations (in contrast with the multiple duplicated alleles found in Culex pipiens mosquitoes). We used a new approach, combining long and short-read sequencing with Sanger sequencing to precisely identify and describe at least nine different heterogeneous duplications, in two populations of An. gambiae s.l. We show that these alleles share the same structure as the previously identified heterogeneous and homogeneous duplications, namely 203-kb tandem amplifications with conserved breakpoints. Our study sheds new light on the origin and maintenance of these alleles in An. gambiae s.l. populations, and their role in mosquito adaptation.
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Affiliation(s)
| | | | - Alice Namias
- ISEM, Université de Montpellier, CNRS, IRD, Montpellier, France
| | - Benoit Assogba
- Medical Research Council, Unit The Gambia at London School of Hygiene and Tropical Medicine, London, UK
| | | | - Alphonsine Koffi
- National Institute of Public Health/Pierre Richet Institute, Bouake, Côte d'Ivoire
| | | | - Mylène Weill
- ISEM, Université de Montpellier, CNRS, IRD, Montpellier, France
| | - Pascal Milesi
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
- Science for Life Laboratory (SciLifeLab), Uppsala University, 75237, Uppsala, Sweden
| | - Pierrick Labbé
- ISEM, Université de Montpellier, CNRS, IRD, Montpellier, France.
- Institut Universitaire de France (IUF), Paris, France.
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5
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Pagnoncelli Jr FDB, Losada FB, Alvear MJG, Gonzalez-Andujar JL, Trezzi MM, Bittencourt HVH, Salomão HM. Response characterization and target site mechanism study in glyphosate-resistant populations of Lolium multiflorum L. from Brazil. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2024; 198:105737. [PMID: 38225083 DOI: 10.1016/j.pestbp.2023.105737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/03/2023] [Accepted: 12/05/2023] [Indexed: 01/17/2024]
Abstract
Italian ryegrass (Lolium multiflorum L.) is an invasive species widely spread in croplands worldwide. The intensive use of glyphosate has resulted in the selection of resistance to this herbicide in Italian ryegrass. This work characterized the response to glyphosate of Italian ryegrass populations from the South and Southwest regions of Paraná, Brazil. A total of 44 Italian ryegrass populations were collected in farming areas, and were classified for glyphosate resistance with 75% of populations resistant to gloyphosate. Of these, 3 resistant (VT05AR, MR20AR and RN01AR) and three susceptible (VT07AS, MR05AS and RN01AS) of these populations were selected to determine the resistance level and the involvement of the target site mechanisms for glyphosate resistance. Susceptible populations GR50 ranged from 165.66 to 218.17 g.e.a. ha-1 and resistant populations from 569.37 to 925.94, providing RI ranging from 2.88 and 4.70. No mutation in EPSPS was observed in the populations, however, in two (MR20AR and RN02AR) of the three resistant populations, an increase in the number of copies of the EPSPs gene (11 to 57×) was detected. The number of copies showed a positive correlation with the gene expression (R2 = 0.86) and with the GR50 of the populations (R2 = 0.81). The increase in EPSPS gene copies contributes to glyphosate resistance in Italian ryegrass populations from Brazil.
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Affiliation(s)
| | - Francisco Barro Losada
- Department of Plant Breeding, Institute for Sustainable Agriculture (IAS-CSIC), Alameda del Obispo, 14004 Cordoba, Spain
| | - Maria Jose Gimenez Alvear
- Department of Plant Breeding, Institute for Sustainable Agriculture (IAS-CSIC), Alameda del Obispo, 14004 Cordoba, Spain
| | - Jose L Gonzalez-Andujar
- Department of Crop Protection, Institute for Sustainable Agriculture (CSIC), Spain and International Laboratory on Global Change (LINCGlobal) (CSIC), Alameda del Obispo, 14005 Cordoba, Spain
| | - Michelangelo Muzell Trezzi
- Department of Agricultural Sciences, Federal Technological University of Paraná, Via do Conhecimento, km 01, 85503-390 Pato Branco, Paraná, Brazil.
| | - Henrique Von Hertwig Bittencourt
- Department of Agronomy, Federal University of Fronteira Sul, BR-158, s/n, Zona Rural, 85301-970-Laranjeiras do Sul, Paraná, Brazil
| | - Helis Marina Salomão
- Department of Agricultural Sciences, Federal Technological University of Paraná, Via do Conhecimento, km 01, 85503-390 Pato Branco, Paraná, Brazil
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6
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Yamada T, Maeda M, Nagai H, Salamin K, Chang YT, Guenova E, Feuermann M, Monod M. Two different types of tandem sequences mediate the overexpression of TinCYP51B in azole-resistant Trichophyton indotineae. Antimicrob Agents Chemother 2023; 67:e0093323. [PMID: 37823662 PMCID: PMC10648874 DOI: 10.1128/aac.00933-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/03/2023] [Indexed: 10/13/2023] Open
Abstract
Trichophyton indotineae is an emerging dermatophyte that causes severe tinea corporis and tinea cruris. Numerous cases of terbinafine- and azole-recalcitrant T. indotineae-related dermatophytosis have been observed in India over the past decade, and cases are now being recorded worldwide. Whole genome sequencing of three azole-resistant strains revealed a variable number of repeats of a 2,404 base pair (bp) sequence encoding TinCYP51B in tandem specifically at the CYP51B locus position. However, many other resistant strains (itraconazole MIC ≥0.25 µg/mL; voriconazole MIC ≥0.25 µg/mL) did not contain such duplications. Whole-genome sequencing of three of these strains revealed a variable number of 7,374 bp tandem repeat blocks harboring TinCYP51B. Consequently, two types of T. indotineae azole-resistant strains were found to host TinCYP51B in tandem sequences (type I with 2,404 bp TinCYP51B blocks and type II with 7,374 bp TinCYP51B blocks). Using the CRISPR/Cas9 genome-editing tool, the copy number of TinCYP51B within the genome of types I and II strains was brought back to a single copy. The azole susceptibility of these modified strains was similar to that of strains without TinCYP51B duplication, showing that azole resistance in T. indotineae strains is mediated by one of two types of TinCYP51B amplification. Type II strains were prevalent among 32 resistant strains analyzed using a rapid and reliable PCR test.
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Affiliation(s)
- Tsuyoshi Yamada
- Teikyo University Institute of Medical Mycology, Tokyo, Japan
- Asia International Institute of Infectious Disease Control, Teikyo University, Tokyo, Japan
| | - Mari Maeda
- Teikyo University Institute of Medical Mycology, Tokyo, Japan
| | | | - Karine Salamin
- Department of Dermatology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Yun-Tsan Chang
- Department of Dermatology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Emmanuella Guenova
- Department of Dermatology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Marc Feuermann
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Michel Monod
- Department of Dermatology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
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7
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Dawe RK. Measuring open chromatin and DNA methylation in repeat arrays. NATURE PLANTS 2023; 9:1379-1380. [PMID: 37640934 DOI: 10.1038/s41477-023-01512-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Affiliation(s)
- R Kelly Dawe
- Department of Plant Biology, University of Georgia, Athens, GA, USA.
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8
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Zhang C, Johnson NA, Hall N, Tian X, Yu Q, Patterson EL. Subtelomeric 5-enolpyruvylshikimate-3-phosphate synthase copy number variation confers glyphosate resistance in Eleusine indica. Nat Commun 2023; 14:4865. [PMID: 37567866 PMCID: PMC10421919 DOI: 10.1038/s41467-023-40407-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Genomic structural variation (SV) has profound effects on organismal evolution; often serving as a source of novel genetic variation. Gene copy number variation (CNV), one type of SV, has repeatedly been associated with adaptive evolution in eukaryotes, especially with environmental stress. Resistance to the widely used herbicide, glyphosate, has evolved through target-site CNV in many weedy plant species, including the economically important grass, Eleusine indica (goosegrass); however, the origin and mechanism of these CNVs remain elusive in many weed species due to limited genetic and genomic resources. To study this CNV in goosegrass, we present high-quality reference genomes for glyphosate-susceptible and -resistant goosegrass lines and fine-assembles of the duplication of glyphosate's target site gene 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS). We reveal a unique rearrangement of EPSPS involving chromosome subtelomeres. This discovery adds to the limited knowledge of the importance of subtelomeres as genetic variation generators and provides another unique example for herbicide resistance evolution.
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Affiliation(s)
- Chun Zhang
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, P.R. China
| | - Nicholas A Johnson
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Nathan Hall
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Xingshan Tian
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, P.R. China.
| | - Qin Yu
- Australian Herbicide Resistance Initiative (AHRI), School of Agriculture and Environment, University of Western Australia (UWA), Perth, Australia.
| | - Eric L Patterson
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, USA.
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9
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Palma-Bautista C, Belluccini P, Vázquez-García JG, Alcántara-de la Cruz R, Barro F, Portugal J, De Prado R. Target-site and non-target-site resistance mechanisms confer multiple resistance to glyphosate and 2,4-D in Carduus acanthoides. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2023; 191:105371. [PMID: 36963940 DOI: 10.1016/j.pestbp.2023.105371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/09/2023] [Accepted: 02/11/2023] [Indexed: 06/18/2023]
Abstract
Carduus acanthoides L. is mainly a range-land weed, but in the 2010s has begun to invade GM crop production systems in Córdoba (Argentina), where glyphosate and 2,4-D have been commonly applied. In 2020, C. acanthoides was found with multiple resistance to these two herbicides. In this study, the mechanisms that confer multiple resistance to glyphosate and 2,4-D, were characterized in one resistant (R) population of C. acanthoides in comparison to a susceptible (S) population. No differences in 14C-herbicide absorption and translocation were observed between R and S populations. In addition, 14C-glyphosate was well translocated to the shoots (∼30%) and roots (∼16%) in both R and S plants, while most of 14C-2,4-D remained restricted in the treated leaf. Glyphosate metabolism did not contribute to resistance of the R population; however, as corroborated by malathion pretreatment, the mechanism of resistance to 2,4-D was enhanced metabolism (63% of the herbicide) mediated by cytochrome P450 (Cyt-P450). No differences were found in baseline EPSPS activity, copy number, and/or gene expression between the R and S populations, but a Pro-106-Ser mutation in EPSPS was present in the R population. Multiple resistances in the R population of C. acanthoides from Argentina were governed by target site resistance (a Pro-106 mutation for glyphosate) and non-target site resistance (Cyt-P450-based metabolic resistance for 2,4-D) mechanisms. This is the first case of resistance to glyphosate and 2,4-D confirmed for this weed in the world.
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Affiliation(s)
- Candelario Palma-Bautista
- Department Agroforestry, Biochemistry and Molecular Biology, University of Cordoba, Córdoba 14071, Spain
| | - Pablo Belluccini
- INTA, Marcos Juárez, Provincial Route 12, Marcos Juarez, Cordoba 2580, Argentina
| | - José G Vázquez-García
- Department Agroforestry, Biochemistry and Molecular Biology, University of Cordoba, Córdoba 14071, Spain
| | - Ricardo Alcántara-de la Cruz
- Centro de Ciências da Natureza, Campus Lagoa do Sino, Universidade Federal de São Carlos, Buri 18290-000, Brazil.
| | - Francisco Barro
- Institute for Sustainable Agriculture, CSIC, Córdoba 14080, Spain
| | - João Portugal
- Biosciences Department, Polytechnic Institute of Beja, Beja 7800-295, Portugal; VALORIZA-Research Centre for Endogenous Resource Valorization, Polytechnic Institute of Portalegre, Portalegre 7300-555, Portugal
| | - Rafael De Prado
- Department Agroforestry, Biochemistry and Molecular Biology, University of Cordoba, Córdoba 14071, Spain
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10
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Herrmann JA, Koprowska A, Winters TJ, Villanueva N, Nikityuk VD, Pek F, Reis EM, Dominguez CZ, Davis D, McPherson E, Rocco SR, Recendez C, Difuntorum SM, Faeth K, Lopez MD, Awwad HM, Ghobashy RA, Cappiello L, Neidle EL, Quiñones-Soto S, Reams AB. Gene amplification mutations originate prior to selective stress in Acinetobacter baylyi. G3 (BETHESDA, MD.) 2023; 13:jkac327. [PMID: 36504387 PMCID: PMC9997567 DOI: 10.1093/g3journal/jkac327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 08/23/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022]
Abstract
The controversial theory of adaptive amplification states gene amplification mutations are induced by selective environments where they are enriched due to the stress caused by growth restriction on unadapted cells. We tested this theory with three independent assays using an Acinetobacter baylyi model system that exclusively selects for cat gene amplification mutants. Our results demonstrate all cat gene amplification mutant colonies arise through a multistep process. While the late steps occur during selection exposure, these mutants derive from low-level amplification mutant cells that form before growth-inhibiting selection is imposed. During selection, these partial mutants undergo multiple secondary steps generating higher amplification over several days to multiple weeks to eventually form visible high-copy amplification colonies. Based on these findings, amplification in this Acinetobacter system can be explained by a natural selection process that does not require a stress response. These findings have fundamental implications to understanding the role of growth-limiting selective environments on cancer development. We suggest duplication mutations encompassing growth factor genes may serve as new genomic biomarkers to facilitate early cancer detection and treatment, before high-copy amplification is attained.
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Affiliation(s)
- Jennifer A Herrmann
- Department of Biological Sciences, California State University, Sacramento, CA 95819-6077, USA
| | - Agata Koprowska
- Department of Biological Sciences, California State University, Sacramento, CA 95819-6077, USA
| | - Tesa J Winters
- Department of Biological Sciences, California State University, Sacramento, CA 95819-6077, USA
| | - Nancy Villanueva
- Department of Biological Sciences, California State University, Sacramento, CA 95819-6077, USA
| | - Victoria D Nikityuk
- Department of Biological Sciences, California State University, Sacramento, CA 95819-6077, USA
| | - Feini Pek
- Department of Mathematics and Statistics, California State University, Sacramento, CA 95819-6051, USA
| | - Elizabeth M Reis
- Department of Biological Sciences, California State University, Sacramento, CA 95819-6077, USA
| | - Constancia Z Dominguez
- Department of Biological Sciences, California State University, Sacramento, CA 95819-6077, USA
| | - Daniel Davis
- Department of Biological Sciences, California State University, Sacramento, CA 95819-6077, USA
| | - Eric McPherson
- Department of Biological Sciences, California State University, Sacramento, CA 95819-6077, USA
| | - Staci R Rocco
- Department of Biological Sciences, California State University, Sacramento, CA 95819-6077, USA
| | - Cynthia Recendez
- Department of Biological Sciences, California State University, Sacramento, CA 95819-6077, USA
| | - Shyla M Difuntorum
- Department of Biological Sciences, California State University, Sacramento, CA 95819-6077, USA
| | - Kelly Faeth
- Department of Biological Sciences, California State University, Sacramento, CA 95819-6077, USA
| | - Mario D Lopez
- Department of Biological Sciences, California State University, Sacramento, CA 95819-6077, USA
| | - Habeeba M Awwad
- Department of Biological Sciences, California State University, Sacramento, CA 95819-6077, USA
| | - Rola A Ghobashy
- Department of Biological Sciences, California State University, Sacramento, CA 95819-6077, USA
| | - Lauren Cappiello
- Department of Mathematics and Statistics, California State University, Sacramento, CA 95819-6051, USA
| | - Ellen L Neidle
- Department of Microbiology, University of Georgia, Athens, GA 30602-2605, USA
| | - Semarhy Quiñones-Soto
- Department of Biological Sciences, California State University, Sacramento, CA 95819-6077, USA
| | - Andrew B Reams
- Department of Biological Sciences, California State University, Sacramento, CA 95819-6077, USA
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11
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Yanniccari M, Palma-Bautista C, Vázquez-García JG, Gigón R, Mallory-Smith CA, De Prado R. Constitutive overexpression of EPSPS by gene duplication is involved in glyphosate resistance in Salsola tragus. PEST MANAGEMENT SCIENCE 2023; 79:1062-1068. [PMID: 36327342 DOI: 10.1002/ps.7272] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/28/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Glyphosate-resistant Salsola tragus accessions have been identified in the USA and Argentina; however, the mechanisms of glyphosate resistance have not been elucidated. The goal of this study was to determine the mechanism/s of glyphosate resistance involved in two S. tragus populations (R1 and R2) from Argentina. RESULTS Both glyphosate-resistant populations had a six-fold lower sensitivity to glyphosate than the S population (i.e. resistance index). No evidence of differential absorption, translocation or metabolism of glyphosate was found in the R1 and R2 populations compared to a susceptible population (S). No 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) mutations were detected, but S. tragus R1 and R2 plants had ≈14-fold higher EPSPS gene relative copy number compared to the S counterpart. In R1 and R2, EPSPS duplication entailed a greater constitutive EPSPS transcript abundance by approximately seven-fold and a basal EPSPS activity approximately three-fold higher than the S population. CONCLUSION The current study reports EPSPS gene duplication for the first time as a mechanism of glyphosate resistance in S. tragus populations. The increase of glyphosate dose needed to kill R1 and R2 plants was linked to the EPSPS transcript abundance and level of EPSPS activity. This evidence supports the convergent evolution of the overexpression of the EPSPS gene in several Chenopodiaceae/Amaranthaceae species adapted to drought environments and the role of gene duplication as an adaptive advantage for plants to withstand stress. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Marcos Yanniccari
- Chacra Experimental Integrada Barrow (MDA-INTA), National Scientific and Technical Research Council (CONICET), Faculty of Agronomy, National University of La Pampa, La Pampa, Argentina
| | - Candelario Palma-Bautista
- Department of Agroforestry, Plant Biochemistry and Molecular Biology, University of Cordoba, Cordoba, Spain
| | | | - Ramón Gigón
- Private Consultant in Weed Control, Tres Arroyos, Argentina
| | | | - Rafael De Prado
- Department of Agroforestry, Plant Biochemistry and Molecular Biology, University of Cordoba, Cordoba, Spain
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12
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Kesel E, Hudson AO, Osier MV. Whole-Genome Sequence, Assembly and Annotation of an Invasive Plant, Lonicera maackii (Amur Honeysuckle). PLANTS (BASEL, SWITZERLAND) 2022; 11:3253. [PMID: 36501292 PMCID: PMC9740181 DOI: 10.3390/plants11233253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
The invasive species Lonicera maackii (Amur Honeysuckle) is an increasing problem sweeping from the eastern United States toward the west, impacting normal forest development and animal survival across multiple taxa. Little is known about the genomics of this species, although a related invasive, Lonicera japonica, has been sequenced. Understanding the genomic foundation of the Lonicera maackii species could help us understand the biochemistry and life history that are the underpinnings of invasive success, as well as potential vulnerabilities and strengths which could guide research and development to control its spread. Here we present a draft, but high-quality, short-read whole-genome sequence, assembly, and annotation of Lonicera maackii, demonstrating that inexpensive and rapid short-read technologies can be successfully used in invasive species research. Despite being a short-read assembly, the genome length (7.93 × 108) and completeness (estimated as 90.2-92.1% by BUSCO and Merqury) are close to the previously published chromosome-level sequencing of L. japonica. No bias, by means of a Gene Ontology analysis, was identified among missing BUSCOs. A duplication of the 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase gene in both Lonicera species is identified, and the potential impact on controlling these invasive species is discussed. Future prospects for a diversity analysis of invasive species is also discussed.
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13
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Noguera MM, Porri A, Werle IS, Heiser J, Brändle F, Lerchl J, Murphy B, Betz M, Gatzmann F, Penkert M, Tuerk C, Meyer L, Roma-Burgos N. Involvement of glutamine synthetase 2 (GS2) amplification and overexpression in Amaranthus palmeri resistance to glufosinate. PLANTA 2022; 256:57. [PMID: 35960361 PMCID: PMC9374794 DOI: 10.1007/s00425-022-03968-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 07/24/2022] [Indexed: 06/15/2023]
Abstract
Amplification and overexpression of the target site glutamine synthetase, specifically the plastid-located isoform, confers resistance to glufosinate in Amaranthus palmeri. This mechanism is novel among glufosinate-resistant weeds. Amaranthus palmeri has recently evolved resistance to glufosinate herbicide. Several A. palmeri populations from Missouri and Mississippi, U.S.A. had survivors when sprayed with glufosinate-ammonium (GFA, 657 g ha-1). One population, MO#2 (fourfold resistant) and its progeny (sixfold resistant), were used to study the resistance mechanism, focusing on the herbicide target glutamine synthetase (GS). We identified four GS genes in A. palmeri; three were transcribed: one coding for the plastidic protein (GS2) and two coding for cytoplasmic isoforms (GS1.1 and GS1.2). These isoforms did not contain mutations associated with resistance. The 17 glufosinate survivors studied showed up to 21-fold increase in GS2 copies. GS2 was expressed up to 190-fold among glufosinate survivors. GS1.1 was overexpressed > twofold in only 3 of 17, and GS1.2 in 2 of 17 survivors. GS inhibition by GFA causes ammonia accumulation in susceptible plants. Ammonia level was analyzed in 12 F1 plants. GS2 expression was negatively correlated with ammonia level (r = - 0.712); therefore, plants with higher GS2 expression are less sensitive to GFA. The operating efficiency of photosystem II (ϕPSII) of Nicotiana benthamiana overexpressing GS2 was four times less inhibited by GFA compared to control plants. Therefore, increased copy and overexpression of GS2 confer resistance to GFA in A. palmeri (or other plants). We present novel understanding of the role of GS2 in resistance evolution to glufosinate.
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Affiliation(s)
- Matheus M Noguera
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, 1371 W Altheimer Dr, Fayetteville, AR, 72704, USA
| | - Aimone Porri
- BASF SE, Agricultural Research Station, Limburgerhof, Germany
| | - Isabel S Werle
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, 1371 W Altheimer Dr, Fayetteville, AR, 72704, USA
- Department of Crop Sciences, University of Illinois, Champaign, USA
| | - James Heiser
- Fisher Delta Research Center, University of Missouri, Portageville, MO, USA
| | | | - Jens Lerchl
- BASF SE, Agricultural Research Station, Limburgerhof, Germany
| | - Brent Murphy
- BASF SE, Agricultural Research Station, Limburgerhof, Germany
| | - Michael Betz
- BASF SE, Agricultural Research Station, Limburgerhof, Germany
| | - Fanny Gatzmann
- BASF SE, Agricultural Research Station, Limburgerhof, Germany
| | - Martin Penkert
- BASF SE, Agricultural Research Station, Limburgerhof, Germany
| | - Clara Tuerk
- BASF SE, Agricultural Research Station, Limburgerhof, Germany
| | - Lucie Meyer
- BASF SE, Agricultural Research Station, Limburgerhof, Germany
| | - Nilda Roma-Burgos
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, 1371 W Altheimer Dr, Fayetteville, AR, 72704, USA.
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14
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Grau D, Grau N, Gascuel Q, Paroissin C, Stratonovitch C, Lairon D, Devault DA, Di Cristofaro J. Quantifiable urine glyphosate levels detected in 99% of the French population, with higher values in men, in younger people, and in farmers. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:32882-32893. [PMID: 35018595 PMCID: PMC9072501 DOI: 10.1007/s11356-021-18110-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 12/10/2021] [Indexed: 05/05/2023]
Abstract
France is the first pesticide-consuming country in Europe. Glyphosate is the most used pesticide worldwide and glyphosate is detected in the general population of industrialized countries, with higher levels found in farmers and children. Little data was available concerning exposure in France. Our objective was to determine glyphosate levels in the French general population and to search for an association with seasons, biological features, lifestyle status, dietary habits, and occupational exposure. This study includes 6848 participants recruited between 2018 and 2020. Associated data include age, gender, location, employment status, and dietary information. Glyphosate was quantified by a single laboratory in first-void urine samples using ELISA. Our results support a general contamination of the French population, with glyphosate quantifiable in 99.8% of urine samples with a mean of 1.19 ng/ml + / - 0.84 after adjustment to body mass index (BMI). We confirm higher glyphosate levels in men and children. Our results support glyphosate contamination through food and water intake, as lower glyphosate levels are associated with dominant organic food intake and filtered water. Higher occupational exposure is confirmed in farmers and farmers working in wine-growing environment. Thus, our present results show a general contamination of the French population with glyphosate, and further contribute to the description of a widespread contamination in industrialized countries.
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Affiliation(s)
- Daniel Grau
- Association Campagne Glyphosate, Foix, France
| | - Nicole Grau
- Association Campagne Glyphosate, Foix, France
| | | | | | - Cécile Stratonovitch
- ARSEAA, Pôle Guidance Infantile, Psychiatrie Infanto-juvénile Secteur III, Labège, France
| | - Denis Lairon
- Faculté de Médecine de La Timone, Aix Marseille Université, INSERM, INRA, C2VN, Marseille, France
| | - Damien A Devault
- Centre Universitaire de Formation Et de Recherche de Mayotte, Dembeni, Mayotte, France
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15
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Barco-Antoñanzas M, Gil-Monreal M, Eceiza MV, Royuela M, Zabalza A. Primary metabolism in an Amaranthus palmeri population with multiple resistance to glyphosate and pyrithiobac herbicides. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 318:111212. [PMID: 35351301 DOI: 10.1016/j.plantsci.2022.111212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 02/04/2022] [Accepted: 02/06/2022] [Indexed: 06/14/2023]
Abstract
The objective of this work was to characterize the resistance mechanisms and the primary metabolism of a multiple resistant (MR) population of Amaranthus palmeri to glyphosate and to the acetolactate synthase (ALS) inhibitor pyrithiobac. All MR plants analysed were glyphosate-resistant due to 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene amplification. Resistance to pyrithiobac was more variable among individuals and was related to point mutations at five positions in the ALS gene sequence: A122, A205, W574, S653 and G654. All MR plants were heterozygous for W574, the most abundant mutation. In nontreated plants, the presence of mutations did not affect ALS functionality, and plants with the W574L mutation showed the highest ALS resistance level to pyrithiobac. The accumulation of the transcripts corresponding to several genes of the aromatic amino acid (AAA) and branched-chain amino acid (BCAA) pathways detected in nontreated MR plants indicated additional effects of EPSPS gene amplification and ALS mutations. The physiological performance of the MR population after treatment with glyphosate and/or pyrithiobac was compared with that of a sensitive (S) population. The increase induced in total soluble sugars, AAA or BCAA content by both herbicides was higher in the S population than in the MR population. Physiological effects were not exacerbated after the mixture of both herbicides in S or in MR populations. This study provides new insights into the physiology of a multiple resistant A. palmeri, which could be very useful for achieving effective management of this weed.
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Affiliation(s)
- María Barco-Antoñanzas
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Universidad Pública de Navarra (UPNA), Campus de Arrosadía, E-31006 Pamplona, Spain
| | - Miriam Gil-Monreal
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Universidad Pública de Navarra (UPNA), Campus de Arrosadía, E-31006 Pamplona, Spain
| | - Mikel V Eceiza
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Universidad Pública de Navarra (UPNA), Campus de Arrosadía, E-31006 Pamplona, Spain
| | - Mercedes Royuela
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Universidad Pública de Navarra (UPNA), Campus de Arrosadía, E-31006 Pamplona, Spain
| | - Ana Zabalza
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Universidad Pública de Navarra (UPNA), Campus de Arrosadía, E-31006 Pamplona, Spain.
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16
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Ruszkowski M, Forlani G. Deciphering the Structure of Arabidopsis thaliana 5-enol-Pyruvyl-Shikimate-3-Phosphate Synthase: an Essential Step toward the Discovery of Novel Inhibitors to Supersede Glyphosate. Comput Struct Biotechnol J 2022; 20:1494-1505. [PMID: 35422967 PMCID: PMC8983318 DOI: 10.1016/j.csbj.2022.03.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 03/19/2022] [Accepted: 03/21/2022] [Indexed: 11/19/2022] Open
Abstract
Glyphosate interferes with plant aromatic metabolism through the inhibition of 5-enol-pyruvyl-shikimate-3-phosphate (EPSP) synthase [EPSPS, EC 2.5.1.19]. For this reason, EPSPS has been extensively studied in a vast array of organisms. This notwithstanding, up to date, the crystal structure of the protein has been solved exclusively in a few prokaryotes, while that of the plant enzyme has been only deduced in silico by similarity. This study aimed at determining the structure of EPSPS from the plant model species Arabidopsis thaliana, which has been cloned, heterologously expressed and affinity-purified. The kinetic properties of the enzyme have been determined, as well as its susceptibility to the inhibition brought about by glyphosate. The crystal structure of the protein has been resolved at high resolution (1.4 Å), showing open conformation of the enzyme, which is the state ready for substrate/inhibitor binding. This provides a framework for the structure-based design of novel EPSPS inhibitors. Surface regions near the active-site cleft entrance or at the interdomain hinge appear promising for inhibitor selectivity, while bound chloride near the active site is a potential placeholder for anionic moieties of future herbicides.
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Affiliation(s)
- Milosz Ruszkowski
- Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Synchrotron Radiation Research Section of MCL, National Cancer Institute, Argonne, IL, USA
- Corresponding author at: Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
| | - Giuseppe Forlani
- Department of Life Science and Biotechnology, University of Ferrara, Ferrara, Italy
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17
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Wu D, Shen E, Jiang B, Feng Y, Tang W, Lao S, Jia L, Lin HY, Xie L, Weng X, Dong C, Qian Q, Lin F, Xu H, Lu H, Cutti L, Chen H, Deng S, Guo L, Chuah TS, Song BK, Scarabel L, Qiu J, Zhu QH, Yu Q, Timko MP, Yamaguchi H, Merotto A, Qiu Y, Olsen KM, Fan L, Ye CY. Genomic insights into the evolution of Echinochloa species as weed and orphan crop. Nat Commun 2022; 13:689. [PMID: 35115514 PMCID: PMC8814039 DOI: 10.1038/s41467-022-28359-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/20/2022] [Indexed: 12/20/2022] Open
Abstract
As one of the great survivors of the plant kingdom, barnyard grasses (Echinochloa spp.) are the most noxious and common weeds in paddy ecosystems. Meanwhile, at least two Echinochloa species have been domesticated and cultivated as millets. In order to better understand the genomic forces driving the evolution of Echinochloa species toward weed and crop characteristics, we assemble genomes of three Echinochloa species (allohexaploid E. crus-galli and E. colona, and allotetraploid E. oryzicola) and re-sequence 737 accessions of barnyard grasses and millets from 16 rice-producing countries. Phylogenomic and comparative genomic analyses reveal the complex and reticulate evolution in the speciation of Echinochloa polyploids and provide evidence of constrained disease-related gene copy numbers in Echinochloa. A population-level investigation uncovers deep population differentiation for local adaptation, multiple target-site herbicide resistance mutations of barnyard grasses, and limited domestication of barnyard millets. Our results provide genomic insights into the dual roles of Echinochloa species as weeds and crops as well as essential resources for studying plant polyploidization, adaptation, precision weed control and millet improvements.
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Affiliation(s)
- Dongya Wu
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Enhui Shen
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
- Zhejiang University Zhongyuan Institute, Zhengzhou, 450000, China
| | - Bowen Jiang
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Yu Feng
- Institute of Ecology, Zhejiang University, Hangzhou, 310058, China
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Wei Tang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Sangting Lao
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Lei Jia
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Han-Yang Lin
- Institute of Ecology, Zhejiang University, Hangzhou, 310058, China
| | - Lingjuan Xie
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Xifang Weng
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Chenfeng Dong
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Qinghong Qian
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Feng Lin
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Haiming Xu
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Huabing Lu
- Institute of Maize and Upland Grain, Zhejiang Academy of Agricultural Sciences, Dongyang, 322105, China
| | - Luan Cutti
- Department of Crop Sciences, Agricultural School, Federal University of Rio Grande do Sul, Porto Alegre, RS, 91540-000, Brazil
| | - Huajun Chen
- College of Computer Science and Technology, Zhejiang University, Hangzhou, 310058, China
| | - Shuiguang Deng
- College of Computer Science and Technology, Zhejiang University, Hangzhou, 310058, China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Tse-Seng Chuah
- Faculty of Plantation and Agrotechnology, Universiti Teknologi MARA, 02600, Arau, Perlis, Malaysia
| | - Beng-Kah Song
- School of Science, Monash University Malaysia, 46150, Bandar Sunway, Selangor, Malaysia
| | - Laura Scarabel
- Istituto per la Protezione Sostenibile delle Piante (IPSP), CNR, Viale dell'Università, 16, 35020, Legnaro (PD), Italy
| | - Jie Qiu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200235, China
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Qin Yu
- Australian Herbicide Resistance Initiative, School of Agriculture and Environment, University of Western Australia, Crawley, WA, 6009, Australia
| | - Michael P Timko
- Department of Biology, University of Virginia, Charlottesville, VA, 22904, USA
| | | | - Aldo Merotto
- Department of Crop Sciences, Agricultural School, Federal University of Rio Grande do Sul, Porto Alegre, RS, 91540-000, Brazil
| | - Yingxiong Qiu
- Institute of Ecology, Zhejiang University, Hangzhou, 310058, China
| | - Kenneth M Olsen
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Longjiang Fan
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
- Zhejiang University Zhongyuan Institute, Zhengzhou, 450000, China
| | - Chu-Yu Ye
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China.
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18
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Heckel DG. Perspectives on gene copy number variation and pesticide resistance. PEST MANAGEMENT SCIENCE 2022; 78:12-18. [PMID: 34480789 DOI: 10.1002/ps.6631] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 07/28/2021] [Accepted: 09/04/2021] [Indexed: 06/13/2023]
Abstract
Although the generation of evolutionary diversity by gene duplication has long been known, the implications for pesticide resistance are just now beginning to be appreciated. A few examples will be cited to illustrate the point that there are many variations on the theme that gene duplication does not follow a set pattern. Transposable elements may facilitate the process but the mechanistic details are obscure and unpredictable. New developments in DNA sequencing technology and genome assembly promise to reveal more examples, yet care must be taken in interpreting the results of transcriptome and genome assemblies and independent means of validation are important. Once a specific gene family is identified, special methods generally must be used to avoid underestimating population polymorphisms and being trapped in preconceptions about the simplicity of the process. © 2021 The Author. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- David G Heckel
- Max Planck Institute for Chemical Ecology, Jena, Germany
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19
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Melero-Jiménez IJ, Bañares-España E, Reul A, Flores-Moya A, García-Sánchez MJ. Detection of the maximum resistance to the herbicides diuron and glyphosate, and evaluation of its phenotypic cost, in freshwater phytoplankton. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2021; 240:105973. [PMID: 34600397 DOI: 10.1016/j.aquatox.2021.105973] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 09/09/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
One of the most important anthropogenic impacts on freshwater aquatic ecosystems close to intensive agriculture areas is the cumulative increase in herbicide concentrations. The threat is especially relevant for phytoplankton organisms because they have the same physiological targets as the plants for which herbicides have been designed. This led us to explore the evolutionary response of three phytoplanktonic species to increasing concentrations of two herbicides and its consequences in terms of growth and photosynthesis performance. Specifically, we used an experimental ratchet protocol to investigate the differential evolution and the limit of resistance of a cyanobacterium (Microcystis aeruginosa) and two chlorophyceans (Chlamydomonas reinhardtii and Dictyosphaerium chlorelloides) to two herbicides in worldwide use: glyphosate and diuron. Initially, the growth rate of M. aeruginosa and D. chlorelloides was completely inhibited when they were exposed to a dose of 0.23 ppm diuron or 40 ppm glyphosate, whereas a higher concentration of both herbicides (0.46 ppm diuron or 90 ppm glyphosate) was necessary to abolish C. reinhardtii growth. However, after running a ratchet protocol, the resistance of the three species to both herbicides increased by an adaptation process. M. aeruginosa and D. chlorelloides were able to grow at 1.84 ppm diuron and 80 ppm glyphosate and C. reinhardtii proliferated at twice these concentrations. Herbicide-resistant strains showed lower growth rates than their wild-type counterparts in the absence of herbicides, as well as changes on morphology and differences on photosynthetic pigment content. Besides, herbicide-resistant cells generally showed a lower photosynthetic performance than wild-type strains in the three species. These results indicate that the introduction of both herbicides in freshwater ecosystems could produce a diminution of primary production due to the selection of herbicide-resistant mutants, that would exhibit lower photosynthetic performance than wild-type populations.
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Affiliation(s)
- Ignacio J Melero-Jiménez
- Departamento de Botánica y Fisiología Vegetal, Universidad de Málaga, Campus de Teatinos s/n, 29071 Málaga, Spain.
| | - Elena Bañares-España
- Departamento de Botánica y Fisiología Vegetal, Universidad de Málaga, Campus de Teatinos s/n, 29071 Málaga, Spain
| | - Andreas Reul
- Departamento de Ecología y Geología, Universidad de Málaga, Campus de Teatinos s/n, 29071 Málaga, Spain
| | - Antonio Flores-Moya
- Departamento de Botánica y Fisiología Vegetal, Universidad de Málaga, Campus de Teatinos s/n, 29071 Málaga, Spain
| | - María J García-Sánchez
- Departamento de Botánica y Fisiología Vegetal, Universidad de Málaga, Campus de Teatinos s/n, 29071 Málaga, Spain
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20
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Turning Waste into Beneficial Resource: Implication of Ageratum conyzoides L. in Sustainable Agriculture, Environment and Biopharma Sectors. Mol Biotechnol 2021; 64:221-244. [PMID: 34628588 PMCID: PMC8502239 DOI: 10.1007/s12033-021-00409-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 09/21/2021] [Indexed: 12/14/2022]
Abstract
The annual herb, Ageratum conyzoides L. (Asteraceae), is distributed throughout the world. Although invasive, it can be very useful as a source of essential oils, pharmaceuticals, biopesticides, and bioenergy. However, very limited information exists on the molecular basis of its different utility as previous investigations were mainly focused on phytochemical/biological activity profiling. Here we have explored various properties of A. conyzoides that may offer environmental, ecological, agricultural, and health benefits. As this aromatic plant harbors many important secondary metabolites that may have various implications, biotechnological interventions such as genomics, metabolomics and tissue-culture can be indispensable tools for their mass-production. Further, A. conyzoides acts as a natural reservoir of begomoviruses affecting a wide range of plant species. As the mechanisms of disease spreading and crop infection are not fully clear, whole-genome sequencing and various advanced molecular technologies including RNAi, CRISPER/Cas9, multi-omics approaches, etc., may aid to decipher the molecular mechanism of such disease development and thus, can be useful in crop protection. Overall, improved knowledge of A. conyzoides is not only essential for developing sustainable weed control strategy but can also offer potential ways for biomedicinal, environment, safe and clean agriculture applications.
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Zhang C, Yu CJ, Yu Q, Guo WL, Zhang TJ, Tian XS. Evolution of multiple target-site resistance mechanisms in individual plants of glyphosate-resistant Eleusine indica from China. PEST MANAGEMENT SCIENCE 2021; 77:4810-4817. [PMID: 34161662 DOI: 10.1002/ps.6527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/08/2021] [Accepted: 06/23/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Glyphosate has been used for weed control in South China in various situations for four decades, and most Eleusine indica populations are suspected to have evolved resistance to glyphosate. This research investigated underling target-site glyphosate resistance mechanisms in six field-collected, putative glyphosate-resistant (R) E. indica populations. RESULTS The six R E. indica populations were confirmed to be low (1.8 to 2.6-fold) to moderately (5.6- to 8.4-fold) resistant to glyphosate relative to the susceptible (S) population. Sixty-seven glyphosate-surviving plants from the six R populations were used to examine target-site resistance mechanisms. Target-site 5-enolpyruvylshikimate3-phosphate synthase (EPSPS) overexpression (OE) (plus further induction by glyphosate treatment) and gene copy number variation (CNV) occurred in 94% R plants, and among them, 16% had the P106A mutation and 49% had the heterozygous double TIPS (T102I + P106S) mutation (plus P381L). In addition, a low number of R plants (6%) only had the homologous TIPS (plus P381L) mutation. The (CT)6 insertion mutation in the EPSPS 5†-UTR always associates with EPSPS OE and CNV. Progeny plants possessing EPSPS OE/CNV (and P106A) displayed low level (up to 4.5-fold) glyphosate resistance. In contrast, plants homozygous for the TIPS mutation displayed higher (25-fold) resistance to glyphosate and followed by plants heterozygous for this mutation plus EPSPS OE/CNV (12-fold). CONCLUSIONS Target-site glyphosate resistance in E. indica populations from South China is common with prevalence of EPSPS OE/induction/CNV conferring low level resistance. Individual plants acquiring both the TIPS mutation and EPSPS OE/CNV are favored due to evolutionary advantages. The role of (CT)6 insertion mutation in EPSPS CNV is worth further investigation. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Chun Zhang
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Chao-Jie Yu
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Qin Yu
- Australian Herbicide Resistance Initiative, School of Agriculture and Environment, University of Western Australia, Perth, WA, Australia
| | - Wen-Lei Guo
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Tai-Jie Zhang
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xing-Shan Tian
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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Lim CA, Jha P, Kumar V, Dyer AT. Effect of EPSPS gene copy number and glyphosate selection on fitness of glyphosate-resistant Bassia scoparia in the field. Sci Rep 2021; 11:16083. [PMID: 34373526 PMCID: PMC8352990 DOI: 10.1038/s41598-021-95517-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 07/22/2021] [Indexed: 11/08/2022] Open
Abstract
The widespread evolution of glyphosate-resistant (GR) Bassia scoparia in the U.S. Great Plains poses a serious threat to the long-term sustainability of GR sugar beet. Glyphosate resistance in B. scoparia is due to an increase in the EPSPS (5-enolpyruvyl-shikimate-3-phosphate) gene copy number. The variation in EPSPS gene copies among individuals from within a single GR B. scoparia population indicated a differential response to glyphosate selection. With the continued use of glyphosate in GR sugar beet, the effect of increasing glyphosate rates (applied as single or sequential applications) on the fitness of GR B. scoparia individuals with variable EPSPS gene copies was tested under field conditions. The variation in EPSPS gene copy number and total glyphosate rate (single or sequential applications) did not influence any of the reproductive traits of GR B. scoparia, except seed production. Sequential applications of glyphosate with a total rate of 2214 g ae ha-1 or higher prevented seed production in B. scoparia plants with 2-4 (low levels of resistance) and 5-6 (moderate levels of resistance) EPSPS gene copies. Timely sequential applications of glyphosate (full recommended rates) can potentially slow down the evolution of GR B. scoparia with low to moderate levels of resistance (2-6 EPSPS gene copies), but any survivors (highly-resistant individuals with ≥ 8 EPSPS gene copies) need to be mechanically removed before flowering from GR sugar beet fields. This research warrants the need to adopt ecologically based, multi-tactic strategies to reduce exposure of B. scoparia to glyphosate in GR sugar beet.
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Affiliation(s)
- Charlemagne Ajoc Lim
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
| | - Prashant Jha
- Department of Agronomy, Iowa State University, Ames, IA, USA.
| | - Vipan Kumar
- Agricultural Research Center, Kansas State University, Hays, KS, USA
| | - Alan T Dyer
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
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Cockerton HM, Kaundun SS, Nguyen L, Hutchings SJ, Dale RP, Howell A, Neve P. Fitness Cost Associated With Enhanced EPSPS Gene Copy Number and Glyphosate Resistance in an Amaranthus tuberculatus Population. FRONTIERS IN PLANT SCIENCE 2021; 12:651381. [PMID: 34267768 PMCID: PMC8276266 DOI: 10.3389/fpls.2021.651381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 06/02/2021] [Indexed: 06/13/2023]
Abstract
The evolution of resistance to pesticides in agricultural systems provides an opportunity to study the fitness costs and benefits of novel adaptive traits. Here, we studied a population of Amaranthus tuberculatus (common waterhemp), which has evolved resistance to glyphosate. The growth and fitness of seed families with contrasting levels of glyphosate resistance was assessed in the absence of glyphosate to determine their ability to compete for resources under intra- and interspecific competition. We identified a positive correlation between the level of glyphosate resistance and gene copy number for the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) glyphosate target, thus identifying gene amplification as the mechanism of resistance within the population. Resistant A. tuberculatus plants were found to have a lower competitive response when compared to the susceptible phenotypes with 2.76 glyphosate resistant plants being required to have an equal competitive effect as a single susceptible plant. A growth trade-off was associated with the gene amplification mechanism under intra-phenotypic competition where 20 extra gene copies were associated with a 26.5 % reduction in dry biomass. Interestingly, this growth trade-off was mitigated when assessed under interspecific competition from maize.
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Affiliation(s)
- Helen M. Cockerton
- NIAB EMR, Kent, United Kingdom
- Warwick Crop Centre, The University of Warwick Wellesbourne, Warwick, United Kingdom
| | - Shiv S. Kaundun
- Syngenta, Jealott’s Hill International Research Centre, Bracknell, United Kingdom
| | | | - Sarah Jane Hutchings
- Syngenta, Jealott’s Hill International Research Centre, Bracknell, United Kingdom
| | - Richard P. Dale
- Syngenta, Jealott’s Hill International Research Centre, Bracknell, United Kingdom
| | - Anushka Howell
- Syngenta, Jealott’s Hill International Research Centre, Bracknell, United Kingdom
| | - Paul Neve
- Warwick Crop Centre, The University of Warwick Wellesbourne, Warwick, United Kingdom
- Rothamsted Research, Harpenden, United Kingdom
- Department of Plant and Environmental Sciences, University of Copenhagen, Tåstrup, Denmark
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24
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Baek Y, Bobadilla LK, Giacomini DA, Montgomery JS, Murphy BP, Tranel PJ. Evolution of Glyphosate-Resistant Weeds. REVIEWS OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2021; 255:93-128. [PMID: 33932185 DOI: 10.1007/398_2020_55] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Widespread adoption of glyphosate-resistant crops and concomitant reliance on glyphosate for weed control set an unprecedented stage for the evolution of herbicide-resistant weeds. There are now 48 weed species that have evolved glyphosate resistance. Diverse glyphosate-resistance mechanisms have evolved, including single, double, and triple amino acid substitutions in the target-site gene, duplication of the gene encoding the target site, and others that are rare or nonexistent for evolved resistance to other herbicides. This review summarizes these resistance mechanisms, discusses what is known about their evolution, and concludes with some of the impacts glyphosate-resistant weeds have had on weed management.
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Affiliation(s)
- Yousoon Baek
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Lucas K Bobadilla
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Darci A Giacomini
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | | | - Brent P Murphy
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Patrick J Tranel
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA.
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25
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Singh V, Etheredge L, McGinty J, Morgan G, Bagavathiannan M. First case of glyphosate resistance in weedy sunflower (Helianthus annuus). PEST MANAGEMENT SCIENCE 2020; 76:3685-3692. [PMID: 32419329 DOI: 10.1002/ps.5917] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 05/02/2020] [Accepted: 05/18/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Weedy sunflower (Helianthus annuus L.) is a troublesome weed in row-crop production fields in South Texas. Populations with suspected resistance to glyphosate were evaluated with 1X and 4X rates (X = 868 g ae ha-1 ) of the herbicide, followed by a dose-response assay of the most resistant population. Molecular studies were conducted to determine if target-site mechanisms were responsible for resistance in these populations. Additionally, field experiments were conducted at two locations (Somerville and Granger, TX) to evaluate the effectiveness of different tank-mix combinations in controlling naturally infesting glyphosate-resistant (GR) weedy sunflower populations in GR corn. RESULTS In a study conducted in the growth chamber, seven of the 11 tested populations survived up to the 4X rate of glyphosate. The most-resistant population (TX15-11) was 29-fold more resistant to glyphosate, compared to the susceptible standard. In resistant populations, 5-21 more copies of the EPSPS gene were observed compared to the susceptible standard. In the field studies, tank-mix applications of glyphosate + halosulfuron-methyl, glyphosate + prosulfuron, glyphosate + a premix of halosulfuron-methyl and dicamba or glyphosate + a premix of diflufenzopyr and dicamba effectively controlled GR weedy sunflower populations. CONCLUSION Glyphosate-resistance was observed in 81% of the putative resistant weedy sunflower populations tested in this study. Resistance in these populations was conferred primarily by amplification of the EPSPS gene. Effective control of GR weedy sunflower can be achieved by tank-mixes tested in the current study, which provides acceptable levels of crop safety. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Vijay Singh
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA
| | | | - Josh McGinty
- AgriLife Research and Extension Center, Texas A&M University, Corpus Christi, TX, USA
| | - Gaylon Morgan
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA
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26
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Molin WT, Patterson EL, Saski CA. Homogeneity among glyphosate-resistant Amaranthus palmeri in geographically distant locations. PLoS One 2020; 15:e0233813. [PMID: 32903277 PMCID: PMC7480871 DOI: 10.1371/journal.pone.0233813] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/10/2020] [Indexed: 02/06/2023] Open
Abstract
Since the initial report of glyphosate-resistant (GR) Amaranthus palmeri S. Watson in 2006, resistant populations have been reported in 28 states. The mechanism of resistance is amplification of a 399-kb extrachromosomal circular DNA, called the EPSPS replicon, and is unique to glyphosate-resistant plants. The replicon contains a single copy of the 10-kb 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene which causes the concomitant increased expression of EPSP synthase, the target enzyme of glyphosate. It is not known whether the resistance by this amplification mechanism evolved once and then spread across the country or evolved independently in several locations. To compare genomic representation and variation across the EPSPS replicon, whole genome shotgun sequencing (WGS) and mapping of sequences from both GR and susceptible (GS) biotypes to the replicon consensus sequence was performed. Sampling of GR biotypes from AZ, KS, GA, MD and DE and GS biotypes from AZ, KS and GA revealed complete contiguity and deep representation with sequences from GR plants, but lack of homogeneity and contiguity with breaks in coverage were observed with sequences from GS biotypes. The high sequence conservation among GR biotypes with very few polymorphisms which were widely distributed across the USA further supports the hypothesis that glyphosate resistance most likely originated from a single population. We show that the replicon from different populations was unique to GR plants and had similar levels of amplification.
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Affiliation(s)
- William T. Molin
- Crop Production Systems Research Unit, United States Department of Agriculture, Stoneville, Mississippi, United States of America
| | - Eric L. Patterson
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan, United States of America
| | - Christopher A. Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, South Carolina, United States of America
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27
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Gaines TA, Duke SO, Morran S, Rigon CAG, Tranel PJ, Küpper A, Dayan FE. Mechanisms of evolved herbicide resistance. J Biol Chem 2020; 295:10307-10330. [PMID: 32430396 PMCID: PMC7383398 DOI: 10.1074/jbc.rev120.013572] [Citation(s) in RCA: 206] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/18/2020] [Indexed: 12/13/2022] Open
Abstract
The widely successful use of synthetic herbicides over the past 70 years has imposed strong and widespread selection pressure, leading to the evolution of herbicide resistance in hundreds of weed species. Both target-site resistance (TSR) and nontarget-site resistance (NTSR) mechanisms have evolved to most herbicide classes. TSR often involves mutations in genes encoding the protein targets of herbicides, affecting the binding of the herbicide either at or near catalytic domains or in regions affecting access to them. Most of these mutations are nonsynonymous SNPs, but polymorphisms in more than one codon or entire codon deletions have also evolved. Some herbicides bind multiple proteins, making the evolution of TSR mechanisms more difficult. Increased amounts of protein target, by increased gene expression or by gene duplication, are an important, albeit less common, TSR mechanism. NTSR mechanisms include reduced absorption or translocation and increased sequestration or metabolic degradation. The mechanisms that can contribute to NTSR are complex and often involve genes that are members of large gene families. For example, enzymes involved in herbicide metabolism-based resistances include cytochromes P450, GSH S-transferases, glucosyl and other transferases, aryl acylamidase, and others. Both TSR and NTSR mechanisms can combine at the individual level to produce higher resistance levels. The vast array of herbicide-resistance mechanisms for generalist (NTSR) and specialist (TSR and some NTSR) adaptations that have evolved over a few decades illustrate the evolutionary resilience of weed populations to extreme selection pressures. These evolutionary processes drive herbicide and herbicide-resistant crop development and resistance management strategies.
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Affiliation(s)
- Todd A Gaines
- Agricultural Biology Department, Colorado State University, Fort Collins, Colorado, USA
| | - Stephen O Duke
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, Oxford, Mississippi, USA
| | - Sarah Morran
- Agricultural Biology Department, Colorado State University, Fort Collins, Colorado, USA
| | - Carlos A G Rigon
- Agricultural Biology Department, Colorado State University, Fort Collins, Colorado, USA
| | - Patrick J Tranel
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA
| | - Anita Küpper
- Bayer AG, CropScience Division, Frankfurt am Main, Germany
| | - Franck E Dayan
- Agricultural Biology Department, Colorado State University, Fort Collins, Colorado, USA
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28
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Trouern-Trend AJ, Falk T, Zaman S, Caballero M, Neale DB, Langley CH, Dandekar AM, Stevens KA, Wegrzyn JL. Comparative genomics of six Juglans species reveals disease-associated gene family contractions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:410-423. [PMID: 31823432 DOI: 10.1111/tpj.14630] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 11/01/2019] [Indexed: 06/10/2023]
Abstract
Juglans (walnuts), the most speciose genus in the walnut family (Juglandaceae), represents most of the family's commercially valuable fruit and wood-producing trees. It includes several species used as rootstock for their resistance to various abiotic and biotic stressors. We present the full structural and functional genome annotations of six Juglans species and one outgroup within Juglandaceae (Juglans regia, J. cathayensis, J. hindsii, J. microcarpa, J. nigra, J. sigillata and Pterocarya stenoptera) produced using BRAKER2 semi-unsupervised gene prediction pipeline and additional tools. For each annotation, gene predictors were trained using 19 tissue-specific J. regia transcriptomes aligned to the genomes. Additional functional evidence and filters were applied to multi-exonic and mono-exonic putative genes to yield between 27 000 and 44 000 high-confidence gene models per species. Comparison of gene models to the BUSCO embryophyta dataset suggested that, on average, genome annotation completeness was 85.6%. We utilized these high-quality annotations to assess gene family evolution within Juglans, and among Juglans and selected Eurosid species. We found notable contractions in several gene families in J. hindsii, including disease resistance-related wall-associated kinase (WAK), Catharanthus roseus receptor-like kinase (CrRLK1L) and others involved in abiotic stress response. Finally, we confirmed an ancient whole-genome duplication that took place in a common ancestor of Juglandaceae using site substitution comparative analysis.
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Affiliation(s)
| | - Taylor Falk
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Sumaira Zaman
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Madison Caballero
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - David B Neale
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - Charles H Langley
- Department of Evolution and Ecology, University of California Davis, Davis, CA, USA
| | - Abhaya M Dandekar
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - Kristian A Stevens
- Department of Evolution and Ecology, University of California Davis, Davis, CA, USA
- Department of Computer Science, University of California Davis, Davis, CA, USA
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
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29
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Patterson EL, Saski CA, Sloan DB, Tranel PJ, Westra P, Gaines TA. The Draft Genome of Kochia scoparia and the Mechanism of Glyphosate Resistance via Transposon-Mediated EPSPS Tandem Gene Duplication. Genome Biol Evol 2019; 11:2927-2940. [PMID: 31518388 PMCID: PMC6808082 DOI: 10.1093/gbe/evz198] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2019] [Indexed: 12/14/2022] Open
Abstract
Increased copy number of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene confers resistance to glyphosate, the world's most-used herbicide. There are typically three to eight EPSPS copies arranged in tandem in glyphosate-resistant populations of the weed kochia (Kochia scoparia). Here, we report a draft genome assembly from a glyphosate-susceptible kochia individual. Additionally, we assembled the EPSPS locus from a glyphosate-resistant kochia plant by sequencing select bacterial artificial chromosomes from a kochia bacterial artificial chromosome library. Comparing the resistant and susceptible EPSPS locus allowed us to reconstruct the history of duplication in the structurally complex EPSPS locus and uncover the genes that are coduplicated with EPSPS, several of which have a corresponding change in transcription. The comparison between the susceptible and resistant assemblies revealed two dominant repeat types. Additionally, we discovered a mobile genetic element with a FHY3/FAR1-like gene predicted in its sequence that is associated with the duplicated EPSPS gene copies in the resistant line. We present a hypothetical model based on unequal crossing over that implicates this mobile element as responsible for the origin of the EPSPS gene duplication event and the evolution of herbicide resistance in this system. These findings add to our understanding of stress resistance evolution and provide an example of rapid resistance evolution to high levels of environmental stress.
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Affiliation(s)
- Eric L Patterson
- Department of Bioagricultural Sciences and Pest Management, Colorado State University
- Department of Genetics and Biochemistry, Clemson University
| | | | | | | | - Philip Westra
- Department of Bioagricultural Sciences and Pest Management, Colorado State University
| | - Todd A Gaines
- Department of Bioagricultural Sciences and Pest Management, Colorado State University
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Multiple modes of convergent adaptation in the spread of glyphosate-resistant Amaranthus tuberculatus. Proc Natl Acad Sci U S A 2019; 116:21076-21084. [PMID: 31570613 PMCID: PMC6800383 DOI: 10.1073/pnas.1900870116] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
While evolution has been thought of as playing out over millions of years, adaptation to new environments can occur very rapidly, presenting us with key opportunities to understand evolutionary dynamics. One of the most amazing examples of real-time evolution comes from agriculture, where due to the intense use of a few herbicides, many plant species have evolved herbicide resistance to become aggressive weeds. An important question has been whether herbicide resistance arises only rarely and then spreads quickly, or whether herbicide resistance arises all the time de novo. Our work with glyphosate resistance in US Midwestern and Canadian populations of Amaranthus tuberculatus reveals the answer to be, “it depends,” as we surprisingly find examples for both modes of evolution. The selection pressure exerted by herbicides has led to the repeated evolution of herbicide resistance in weeds. The evolution of herbicide resistance on contemporary timescales in turn provides an outstanding opportunity to investigate key questions about the genetics of adaptation, in particular the relative importance of adaptation from new mutations, standing genetic variation, or geographic spread of adaptive alleles through gene flow. Glyphosate-resistant Amaranthus tuberculatus poses one of the most significant threats to crop yields in the Midwestern United States, with both agricultural populations and herbicide resistance only recently emerging in Canada. To understand the evolutionary mechanisms driving the spread of resistance, we sequenced and assembled the A. tuberculatus genome and investigated the origins and population genomics of 163 resequenced glyphosate-resistant and susceptible individuals from Canada and the United States. In Canada, we discovered multiple modes of convergent evolution: in one locality, resistance appears to have evolved through introductions of preadapted US genotypes, while in another, there is evidence for the independent evolution of resistance on genomic backgrounds that are historically nonagricultural. Moreover, resistance on these local, nonagricultural backgrounds appears to have occurred predominantly through the partial sweep of a single haplotype. In contrast, resistant haplotypes arising from the Midwestern United States show multiple amplification haplotypes segregating both between and within populations. Therefore, while the remarkable species-wide diversity of A. tuberculatus has facilitated geographic parallel adaptation of glyphosate resistance, more recently established agricultural populations are limited to adaptation in a more mutation-limited framework.
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Gaines TA, Patterson EL, Neve P. Molecular mechanisms of adaptive evolution revealed by global selection for glyphosate resistance. THE NEW PHYTOLOGIST 2019; 223:1770-1775. [PMID: 31002387 DOI: 10.1111/nph.15858] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 04/09/2019] [Indexed: 06/09/2023]
Abstract
The human-directed, global selection for glyphosate resistance in weeds has revealed a fascinating diversity of evolved resistance mechanisms, including herbicide sequestration in the vacuole, a rapid cell death response, nucleotide polymorphisms in the herbicide target (5-enolpyruvylshikimate-3-phosphate synthase, EPSPS) and increased gene copy number of EPSPS. For this latter mechanism, two distinct molecular genetic mechanisms have been observed, a tandem duplication mechanism and a large extrachromosomal circular DNA (eccDNA) that is tethered to the chromosomes and passed to gametes at meiosis. These divergent mechanisms have a range of consequences for the spread, fitness, and inheritance of resistance traits, and, particularly in the case of the eccDNA, demonstrate how evolved herbicide resistance can generate new insights into plant adaptation to contemporary environmental stress.
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Affiliation(s)
- Todd A Gaines
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, 1177 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Eric L Patterson
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, 1177 Campus Delivery, Fort Collins, CO, 80523, USA
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634, USA
| | - Paul Neve
- Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, UK
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32
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Vila-Aiub MM, Yu Q, Powles SB. Do plants pay a fitness cost to be resistant to glyphosate? THE NEW PHYTOLOGIST 2019; 223:532-547. [PMID: 30737790 DOI: 10.1111/nph.15733] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 01/30/2019] [Indexed: 06/09/2023]
Abstract
We reviewed the literature to understand the effects of glyphosate resistance on plant fitness at the molecular, biochemical and physiological levels. A number of correlations between enzyme characteristics and glyphosate resistance imply the existence of a plant fitness cost associated with resistance-conferring mutations in the glyphosate target enzyme, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS). These biochemical changes result in a tradeoff between the glyphosate resistance of the EPSPS enzyme and its catalytic activity. Mutations that endow the highest resistance are more likely to decrease catalytic activity by reducing the affinity of EPSPS for its natural substrate, and/or slowing the velocity of the enzyme reaction, and are thus very likely to endow a substantial plant fitness cost. Prediction of fitness costs associated with EPSPS gene amplification and overexpression can be more problematic. The validity of cost prediction based on the theory of evolution of gene expression and resource allocation has been cast into doubt by contradictory experimental evidence. Further research providing insights into the role of the EPSPS cassette in weed adaptation, and estimations of the energy budget involved in EPSPS amplification and overexpression are required to understand and predict the biochemical and physiological bases of the fitness cost of glyphosate resistance.
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Affiliation(s)
- Martin M Vila-Aiub
- Australian Herbicide Resistance Initiative (AHRI) - School of Agriculture & Environment, University of Western Australia (UWA), Crawley, 6009, Western Australia, Australia
- IFEVA - CONICET - Faculty of Agronomy, Department of Ecology, University of Buenos Aires (UBA), Buenos Aires, 1417, Argentina
| | - Qin Yu
- Australian Herbicide Resistance Initiative (AHRI) - School of Agriculture & Environment, University of Western Australia (UWA), Crawley, 6009, Western Australia, Australia
| | - Stephen B Powles
- Australian Herbicide Resistance Initiative (AHRI) - School of Agriculture & Environment, University of Western Australia (UWA), Crawley, 6009, Western Australia, Australia
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Sablok G, Amiryousefi A, He X, Hyvönen J, Poczai P. Sequencing the Plastid Genome of Giant Ragweed ( Ambrosia trifida, Asteraceae) From a Herbarium Specimen. FRONTIERS IN PLANT SCIENCE 2019; 10:218. [PMID: 30873197 PMCID: PMC6403193 DOI: 10.3389/fpls.2019.00218] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 02/08/2019] [Indexed: 05/09/2023]
Abstract
We report the first plastome sequence of giant ragweed (Ambrosia trifida); with this new genome information, we assessed the phylogeny of Asteraceae and the transcriptional profiling against glyphosate resistance in giant ragweed. Assembly and genic features show a normal angiosperm quadripartite plastome structure with no signatures of deviation in gene directionality. Comparative analysis revealed large inversions across the plastome of giant ragweed and the previously sequenced members of the plant family. Asteraceae plastid genomes contain two inversions of 22.8 and 3.3 kb; the former is located between trnS-GCU and trnG-UCC genes, and the latter between trnE-UUC and trnT-GGU genes. The plastid genome sequences of A. trifida and the related species, Ambrosia artemisiifolia, are identical in gene content and arrangement, but they differ in length. The phylogeny is well-resolved and congruent with previous hypotheses about the phylogenetic relationship of Asteraceae. Transcriptomic analysis revealed divergence in the relative expressions at the exonic and intronic levels, providing hints toward the ecological adaptation of the genus. Giant ragweed shows various levels of glyphosate resistance, with introns displaying higher expression patterns at resistant time points after the assumed herbicide treatment.
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Affiliation(s)
- Gaurav Sablok
- Finnish Museum of Natural History (Botany Unit), University of Helsinki, Helsinki, Finland
- Organismal Evolution and Biology, Faculty of Biology and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Ali Amiryousefi
- Finnish Museum of Natural History (Botany Unit), University of Helsinki, Helsinki, Finland
- Organismal Evolution and Biology, Faculty of Biology and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Xiaolan He
- Finnish Museum of Natural History (Botany Unit), University of Helsinki, Helsinki, Finland
- Organismal Evolution and Biology, Faculty of Biology and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Jaakko Hyvönen
- Finnish Museum of Natural History (Botany Unit), University of Helsinki, Helsinki, Finland
- Organismal Evolution and Biology, Faculty of Biology and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Péter Poczai
- Finnish Museum of Natural History (Botany Unit), University of Helsinki, Helsinki, Finland
- Organismal Evolution and Biology, Faculty of Biology and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
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Palma-Bautista C, Torra J, Garcia MJ, Bracamonte E, Rojano-Delgado AM, Alcántara-de la Cruz R, De Prado R. Reduced Absorption and Impaired Translocation Endows Glyphosate Resistance in Amaranthus palmeri Harvested in Glyphosate-Resistant Soybean from Argentina. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:1052-1060. [PMID: 30624921 DOI: 10.1021/acs.jafc.8b06105] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Amaranthus palmeri S. Watson is probably the worst glyphosate-resistant (GR) weed worldwide. The EPSPS (5-enolpyruvylshikimate-3-phosphate-synthase) gene amplification has been reported as the major target-site-resistance (TSR) mechanism conferring resistance to glyphosate in this species. In this study, TSR and non-target-site-resistance (NTSR) mechanisms to glyphosate were characterized in a putative resistant A. palmeri population (GRP), harvested in a GR soybean crop from Argentina. Glyphosate resistance was confirmed for the GRP population by dose-response assays. No evidence of TSR mechanisms, as well as glyphosate metabolism, was found in this population. Moreover, a susceptible population (GSP) that absorbed about 10% more herbicide than the GRP population was evaluated at different periods after treatment. The GSP population translocated about 20% more glyphosate to the remainder of the shoots and roots at 96 h after treatment than the control, while the GRP population retained 62% of herbicide in the treated leaves. This is the first case of glyphosate resistance in A. palmeri involving exclusively NTSR mechanisms.
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Affiliation(s)
| | - Joel Torra
- Department d'Hortofructicultura, Botànica i Jardineria, Agrotecnio , Universitat de Lleida , 25198 , Lleida , Spain
| | | | - Enzo Bracamonte
- Faculty of Agricultural Sciences , National University of Cordoba (UNC) , 5001 Cordoba , Argentina
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Ravet K, Patterson EL, Krähmer H, Hamouzová K, Fan L, Jasieniuk M, Lawton-Rauh A, Malone JM, McElroy JS, Merotto A, Westra P, Preston C, Vila-Aiub MM, Busi R, Tranel PJ, Reinhardt C, Saski C, Beffa R, Neve P, Gaines TA. The power and potential of genomics in weed biology and management. PEST MANAGEMENT SCIENCE 2018; 74:2216-2225. [PMID: 29687580 DOI: 10.1002/ps.5048] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 04/18/2018] [Accepted: 04/19/2018] [Indexed: 05/11/2023]
Abstract
There have been previous calls for, and efforts focused on, realizing the power and potential of weed genomics for better understanding of weeds. Sustained advances in genome sequencing and assembly technologies now make it possible for individual research groups to generate reference genomes for multiple weed species at reasonable costs. Here, we present the outcomes from several meetings, discussions, and workshops focused on establishing an International Weed Genomics Consortium (IWGC) for a coordinated international effort in weed genomics. We review the 'state of the art' in genomics and weed genomics, including technologies, applications, and on-going weed genome projects. We also report the outcomes from a workshop and a global survey of the weed science community to identify priority species, key biological questions, and weed management applications that can be addressed through greater availability of, and access to, genomic resources. Major focus areas include the evolution of herbicide resistance and weedy traits, the development of molecular diagnostics, and the identification of novel targets and approaches for weed management. There is increasing interest in, and need for, weed genomics, and the establishment of the IWGC will provide the necessary global platform for communication and coordination of weed genomics research. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Karl Ravet
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA
| | - Eric L Patterson
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA
| | | | - Kateřina Hamouzová
- Department of Agroecology and Biometeorology, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Longjiang Fan
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Marie Jasieniuk
- Department of Plant Sciences, University of California-Davis, Davis, CA, USA
| | - Amy Lawton-Rauh
- Department of Genetics and Biochemistry, 316 Biosystems Research Complex, Clemson University, Clemson, SC, USA
| | - Jenna M Malone
- School of Agriculture, Food & Wine, University of Adelaide, Glen Osmond, Australia
| | - J Scott McElroy
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, USA
| | - Aldo Merotto
- Department of Crop Sciences, Agricultural School, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Philip Westra
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA
| | - Christopher Preston
- School of Agriculture, Food & Wine, University of Adelaide, Glen Osmond, Australia
| | - Martin M Vila-Aiub
- Facultad de Agronomía, Departamento de Ecología, IFEVA-CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Roberto Busi
- Australian Herbicide Resistance Initiative, School of Agriculture and Environment, University of Western Australia, Crawley, Australia
| | - Patrick J Tranel
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Carl Reinhardt
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Christopher Saski
- Clemson University Genomics and Computational Biology Laboratory, Clemson University, Clemson, SC, USA
| | - Roland Beffa
- Bayer AG, Industriepark Hoechst, Frankfurt am Main, Germany
| | - Paul Neve
- Biointeractions & Crop Protection Department, Rothamsted Research, West Common, Harpenden, Hertfordshire, UK
| | - Todd A Gaines
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA
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Zhao N, Yan Y, Wang H, Bai S, Wang Q, Liu W, Wang J. Acetolactate Synthase Overexpression in Mesosulfuron-Methyl-Resistant Shortawn Foxtail ( Alopecurus aequalis Sobol.): Reference Gene Selection and Herbicide Target Gene Expression Analysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:9624-9634. [PMID: 30157377 DOI: 10.1021/acs.jafc.8b03054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Severe infestations of shortawn foxtail ( Alopecurus aequalis Sobol.), a noxious weed in wheat and canola cropping systems in China, remain standing even after the application of the herbicides, fenoxaprop- P-ethyl and mesosulfuron-methyl. Analysis of gene expression in weed plants subjected to herbicide treatment is a key step toward more mechanistic studies. Since such an analysis often involves quantitative real-time PCR (qRT-PCR), endogenous reference genes with stable expression are required. Herein, we identified specific gene sets, suitable as references for qRT-PCR data normalization in A. aequalis plants under different experimental conditions, using geNorm, NormFinder, BestKeeper, and RefFinder software. Additionally, the reliability of reference genes was verified by analyzing the expression of genes encoding two major herbicide target enzymes: acetyl-CoA carboxylase (ACCase) and acetolactate synthase (ALS). Furthermore, functional ALS gene amplification was likely present in resistant plants, although it may make no contribution to the resistant phenotypes.
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Affiliation(s)
- Ning Zhao
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection , Shandong Agricultural University , Tai'an 271018 , Shandong , China
| | - Yanyan Yan
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering , Shandong Agricultural University , Tai'an 271018 , Shandong , China
| | - Hengzhi Wang
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection , Shandong Agricultural University , Tai'an 271018 , Shandong , China
| | - Shuang Bai
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection , Shandong Agricultural University , Tai'an 271018 , Shandong , China
| | - Qian Wang
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection , Shandong Agricultural University , Tai'an 271018 , Shandong , China
| | - Weitang Liu
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection , Shandong Agricultural University , Tai'an 271018 , Shandong , China
| | - Jinxin Wang
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection , Shandong Agricultural University , Tai'an 271018 , Shandong , China
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Bracamonte E, Silveira HMD, Alcántara-de la Cruz R, Domínguez-Valenzuela JA, Cruz-Hipolito HE, De Prado R. From tolerance to resistance: mechanisms governing the differential response to glyphosate in Chloris barbata. PEST MANAGEMENT SCIENCE 2018; 74:1118-1124. [PMID: 29384251 DOI: 10.1002/ps.4874] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 01/22/2018] [Accepted: 01/22/2018] [Indexed: 05/11/2023]
Abstract
BACKGROUND Susceptibility and the mechanism (s) governing tolerance/resistance to glyphosate were characterized in two putative-glyphosate-resistant Chloris barbata populations (R1 and R2), collected in Persian lime orchards from Colima State, Mexico, comparing them with one non-treated population (referred to as S). RESULTS Glyphosate doses required to reduce fresh weight or cause mortality by 50% were 4.2-6.4 times higher in resistant populations than in the S population. The S population accumulated 4.3 and 5.2 times more shikimate than the R2 and R1 populations, respectively. There were no differences in 14 C-glyphosate uptake between R and S populations, but the R plants translocated at least 12% less herbicide to the rest of plant and roots 96 h after treatment. Insignificant amounts of glyphosate were metabolized to aminomethyl phosphonate and glyoxylate in both R and S plants. The 5-enolpyruvylshikimate-3-phosphate synthase gene of the R populations contained the Pro106-Ser mutation, giving them a resistance 12 (R2) and 14.7 (R1) times greater at target-site level compared with the S population. CONCLUSION The Pro106-Ser mutation governs the resistance to glyphosate of the R1 and R2 C barbata populations, but the impaired translocation could contribute to the resistance. These results confirm the first case of glyphosate resistance evolved in this species. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Enzo Bracamonte
- Faculty of Agricultural Sciences, National University of Cordoba (UNC), Cordoba, Argentina
| | | | | | | | | | - Rafael De Prado
- Department of Agricultural Chemistry and Edaphology, University of Cordoba, Cordoba, Spain
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